|
| Status |
Public on Dec 15, 2020 |
| Title |
1hrDex_LowDigest_1 MNase-seq |
| Sample type |
SRA |
| |
|
| Source name |
callus on CIM for 5 days with dex treatment
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Landsberg erecta
tissue: callus
transgenic: 35S:LFY-GR
digest: WT
treatment: 1hr Dex treatment
|
| Growth protocol |
Plants were grown on 1/2 MS plates for 3 weeks. Roots were harvested from 3-week-old seedlings and put on CIM for up to 5 days with either 1hr of mock or dex treatment followed by standard ( high) or low MNase digest.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase-seq was conducted using the protocol discribed in Gevry, N., Methods Mol Biol, 2009. Mononuclesoome fractions were isolated and purified.
MNase DNA libraries were generated using the ThruPLEX DNA-seq kit (RUBICON GENOMICS, cat. R400406) and quantified by the NEBNext Library Quant Kit (cat. E7630L). Equal amounts of DNA were pooled from each library with different dual indexing primers and paired-end sequenced on a Next seq 500
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base-calling was performed automatically in Illumina BaseSpace
Trimmed sequencing reads were mapped to Release 10 of the Arabidopsis Genome (TAIR10) using Bowtie v1.2.2 with the `--best -m1 --seed 0` parameters
Paired-end mapped read with fragment size <130 or >170 were removed
Duplicated reads were marked and removed using the MarkDuplicates function in Picard tools 2.9.4
Nucleosome occupancy values of each base pair for each biological replicate wer generated by DANPOS3 using parameter: `--smooth_width 10 -H 1 -m 1 --mifrsz 40 -q 50 -u .1`
For all conditions except 1 hr Dex-LowDigest both biological were analyzed using DANPOS3 and the parameters stated above
For 1hr Dex_LowDigest a merged pooled read was analyzed using DANPOS3 using the parameters stated above
Genome_build: TAIR10
Supplementary_files_format_and_content: *bw: Protein occupancy values of each base pair
Supplementary_files_format_and_content: *bigwig: Protein occupancy values of each base pair averaging two biological replicates
Supplementary_files_format_and_content: *bed: BED file indicating nucleosome regions with DANPOS3 `smt_value` set to score
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Doris Wagner |
| E-mail(s) |
wagnerdo@sas.upenn.edu
|
| Phone |
2158980483
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biology
|
| Lab |
Wagner Lab
|
| Street address |
103G Carolyn Lynch Laboratory
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE141705 |
LFY is pioneer transcription factor [MNase-seq] |
| GSE141706 |
LFY is pioneer transcription factor |
|
| Relations |
| BioSample |
SAMN17025118 |
| SRA |
SRX9648506 |
